In amateur endurance runners, structural changes in the lower limb arteries are rarely documented, with only a few case reports highlighting such findings. This study aimed to explore the incidence of non-atherosclerotic arterial wall changes in a group of amateur male runners and to identify possible correlations with training parameters and biochemical markers. Twenty male athletes, all members of the Black Swan Triathlon Club in Slovakia, who had been engaged in endurance running for over five years, were enrolled in the study. Ultrasound examinations of the tibial and anterior popliteal arteries focused on detecting non-atherosclerotic changes, such as intima-medial border blurring and the presence of nodules. The results revealed that 95% of participants had at least one form of structural abnormality, with intima-medial blurring present in 80% of cases. Nodules were detected in 65% of the runners, with nearly 40% of these nodules classified as hyperechogenic. The abnormalities predominantly affected the popliteal artery and were bilateral in most cases. Interestingly, a mild correlation was observed between the ultrasound findings and training load, such as annual running kilometers and hours. However, no association was found between the arterial changes and lipid levels or C-reactive protein (CRP) levels. These findings suggest that subclinical changes in the lower limb arteries are common in amateur endurance runners, potentially related to increased training load, though the exact mechanisms remain unclear.